Hi,
DAS might work for you - see www.biodas.org for functioning DAS sites.
To get mRNA-to-genome/gene coordinates, I would download tables from
the Santa Cruz Genome Informatics site.
-Ann
On 10/19/05, Charles Hefer <chefer at tuks.co.za> wrote:
> Hi
>> I am looking for a way to automate the retrieval of upstream regions
> of genes (from fully sequenced genomes).
>> I have tried the R/BioMart route, but the organisms I want are not
> available in BioMart (yet). The next option would be to use BLAT to
> retrieve the gene positions and then retrieve the upstream regions, but
> I am looking for a simpler solution. Does one of the Bio modules of i.e
> Python/Java/PERL support this functionality?
>> The aim is to put up a little internal web-service for promoter
> searches, for which the desired gene ID (GenBankId) would be entered and
> the ~2kb upstream region returned.
>> Thanx, in advance
> --
>> Charles
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